/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- *
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.schemes;
-import java.awt.*;
+import jalview.datamodel.AnnotatedCollectionI;
+
+import java.awt.Color;
/**
- * ColourSchemeProperty Binds names to hardwired colourschemes and tries to deal
+ * ColourSchemeProperty binds names to hardwired colourschemes and tries to deal
* intelligently with mapping unknown names to user defined colourschemes (that
* exist or can be created from the string representation of the colourscheme
* name - either a hex RGB triplet or a named colour under java.awt.color ). The
public static final int COVARIATION = 14;
+ public static final int TCOFFEE = 15;
+
+ public static final int RNAHELIX = 16;
+
+ public static final int RNAINTERACTION = 17;
+
/**
* index of first colourscheme (includes 'None')
*/
public static final int FIRST_COLOUR = NONE;
- public static final int LAST_COLOUR = NUCLEOTIDE;
+ public static final int LAST_COLOUR = RNAINTERACTION;
/**
* DOCUMENT ME!
{
ret = NUCLEOTIDE;
}
+ else if (name.equalsIgnoreCase("T-Coffee Scores"))
+ {
+ ret = TCOFFEE;
+ }
+
else if (name.equalsIgnoreCase("User Defined"))
{
ret = USER_DEFINED;
{
ret = NONE;
}
+ else if (name.equalsIgnoreCase("Purine/Pyrimidine"))
+ {
+ ret = PURINEPYRIMIDINE;
+ }
+ else if (name.equalsIgnoreCase("RNA Interaction type"))
+ {
+ ret = RNAINTERACTION;
+ }
+ else if (name.equalsIgnoreCase("RNA Helices"))
+ {
+ ret = RNAHELIX;
+ }
+ // else if (name.equalsIgnoreCase("Covariation"))
+ // {
+ // ret = COVARIATION;
+ // }
return ret;
}
{
index = NUCLEOTIDE;
}
+ else if (cs instanceof PurinePyrimidineColourScheme)
+ {
+ index = PURINEPYRIMIDINE;
+ }
+ else if (cs instanceof TCoffeeColourScheme)
+ {
+ index = TCOFFEE;
+ }
+ else if (cs instanceof RNAHelicesColour)
+ {
+ index = RNAHELIX;
+ }
+ /*
+ * else if (cs instanceof CovariationColourScheme) { index = COVARIATION; }
+ */
else if (cs instanceof UserColourScheme)
{
if ((((UserColourScheme) cs).getName() != null)
break;
+ case PURINEPYRIMIDINE:
+ ret = "Purine/Pyrimidine";
+
+ break;
+
+ case TCOFFEE:
+ ret = "T-Coffee Scores";
+
+ break;
+
+ case RNAINTERACTION:
+ ret = "RNA Interaction type";
+
+ break;
+ case RNAHELIX:
+ ret = "RNA Helices";
+
+ break;
+ /*
+ * case COVARIATION: ret = "Covariation";
+ *
+ * break;
+ */
case USER_DEFINED:
ret = "User Defined";
}
/**
- * DOCUMENT ME!
- *
- * @param al
- * DOCUMENT ME!
- * @param name
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public static ColourSchemeI getColour(jalview.datamodel.AlignmentI al,
- String name)
- {
- return getColour(al.getSequences(), al.getWidth(), name);
- }
-
- /**
* retrieve or create colourscheme associated with name
*
* @param seqs
* string to parse as colour for new coloursheme
* @return Valid Colourscheme
*/
- public static ColourSchemeI getColour(java.util.Vector seqs, int width,
+ public static ColourSchemeI getColour(AnnotatedCollectionI alignment,
String name)
{
int colindex = getColourIndexFromName(name);
}
}
}
- return getColour(seqs, width, getColourIndexFromName(name));
+ return getColour(alignment, getColourIndexFromName(name));
}
/**
- * DOCUMENT ME!
+ * Construct an instance of ColourSchemeI corresponding to the given
+ * colourscheme index
*
* @param seqs
- * DOCUMENT ME!
+ * sequences to be coloured by colourscheme
* @param width
- * DOCUMENT ME!
+ * geometry of alignment
* @param index
- * DOCUMENT ME!
+ * colourscheme number
*
- * @return DOCUMENT ME!
+ * @return null or an instance of the colourscheme configured to colour given
+ * sequence set
*/
- public static ColourSchemeI getColour(java.util.Vector seqs, int width,
- int index)
+ public static ColourSchemeI getColour(
+ jalview.datamodel.AnnotatedCollectionI coll, int index)
{
+ // TODO 3.0 2.8 refactor signature to take an alignmentI like container so
+ // colourschemes based on annotation can be initialised
ColourSchemeI cs = null;
switch (index)
{
case CLUSTAL:
- cs = new ClustalxColourScheme(seqs, width);
+ cs = new ClustalxColourScheme(coll, null);
break;
break;
+ case PURINEPYRIMIDINE:
+ cs = new PurinePyrimidineColourScheme();
+
+ break;
+
+ case TCOFFEE:
+ cs = new TCoffeeColourScheme(coll);
+ break;
+
+ case RNAHELIX:
+ cs = new RNAHelicesColour(coll);
+ break;
+
+ // case COVARIATION:
+ // cs = new CovariationColourScheme(annotation);
+ // break;
+
case USER_DEFINED:
Color[] col = new Color[24];
for (int i = 0; i < 24; i++)
return col;
}
+
+ public static Color rnaHelices[] = null;
+
+ public static void initRnaHelicesShading(int n)
+ {
+ int j = 0;
+ if (rnaHelices == null)
+ {
+ rnaHelices = new Color[n + 1];
+ }
+ else if (rnaHelices != null && rnaHelices.length <= n)
+ {
+ Color[] t = new Color[n + 1];
+ System.arraycopy(rnaHelices, 0, t, 0, rnaHelices.length);
+ j = rnaHelices.length;
+ rnaHelices = t;
+ }
+ else
+ {
+ return;
+ }
+ // Generate random colors and store
+ for (; j <= n; j++)
+ {
+ rnaHelices[j] = jalview.util.ColorUtils
+ .generateRandomColor(Color.white);
+ }
+ }
+
+ /**
+ * delete the existing cached RNA helces colours
+ */
+ public static void resetRnaHelicesShading()
+ {
+ rnaHelices = null;
+ }
+
}
git://source.jalview.org / jalview.git / blobdiff